4DW7
Crystal structure of an active-site mutant of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a CpU dinucleotide
- PDB DOI: https://doi.org/10.2210/pdb4DW7/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Bovine viral diarrhea virus 1-CP7
- Expression System: Drosophila melanogaster
- Mutation(s): Yes 
- Deposited: 2012-02-24 Released: 2012-05-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.08 Å
- R-Value Free: 0.245 
- R-Value Work: 0.197 
- R-Value Observed: 0.200 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
E(rns) glycoprotein | 167 | Bovine viral diarrhea virus 1-CP7 | Mutation(s): 1  Gene Names: Erns | ||
UniProt | |||||
Find proteins for Q96662 (Bovine viral diarrhea virus (strain CP7)) Explore Q96662  Go to UniProtKB:  Q96662 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q96662 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G68945PX GlyCosmos:  G68945PX GlyGen:  G68945PX |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, F, G | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21477HL GlyCosmos:  G21477HL GlyGen:  G21477HL |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
U Query on U | J [auth A], O [auth B] | URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N | |||
C Query on C | K [auth A], P [auth B] | CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N | |||
NAG Query on NAG | H [auth A], I [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.08 Å
- R-Value Free: 0.245 
- R-Value Work: 0.197 
- R-Value Observed: 0.200 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 105.896 | α = 90 |
b = 105.896 | β = 90 |
c = 211.794 | γ = 120 |
Software Name | Purpose |
---|---|
SCALA | data scaling |
PHASER | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
XDS | data reduction |
BUSTER | refinement |
Entry History 
Deposition Data
- Released Date: 2012-05-23  Deposition Author(s): Krey, T., Bontems, F., Vonrhein, C., Vaney, M.-C., Bricogne, G., Ruemenapf, T., Rey, F.A.
Revision History (Full details and data files)
- Version 1.0: 2012-05-23
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary